Matt Ralston

Matt Ralston

M.Sc. Bioinfo + 5 years industry exp. - - - Currently writing a DNA sequence alignment, quasi-mapper, and graph algorithm and manuscript (for bioRxiv). I play math rock on my guitar, I write open-source software on GitHub, I pay my bills in the DE-NJ-PA tri-state area near Delco, and I'm launching a DE-based LLC for Univ. of Delaware and local NGS sequencing projects.

Posts by Category

Coding

Data-literacy

Data-science

Hardware

Opinion

Benchmarking Aligners

1 minute read

Published:

Short-read aligners make up the core of modern bioinformatics program technologies. The aligners are responsible for mapping (rather than aligning) short reads (typically produced by Illumina sequencers) to their most likely originating loci with gapped and ungapped, genomic and transcriptomic methods. For lists of both aligners and short-read mappers and their pros/cons, see the Wikipedia article.

Youth Falls In Night

less than 1 minute read

Published:

I came to life from two unknown trees, Roots tangled deep in mystery’s seas. Yet arms reached out, so strong, so kind, To plant me anew, a love redesigned.

Roots And Wings

less than 1 minute read

Published:

I came to life from two unknown trees, Roots tangled deep in mystery’s seas. Yet arms reached out, so strong, so kind, To plant me anew, a love redesigned.

Ricing In 2024

less than 1 minute read

Published:

Customization is essential for maximizing visual appeal and ease of use of the computer system.

Linear Runtimes For Quasimapping And Alignment Free

1 minute read

Published:

I want to discuss linear runtimes and what that means in alignment-free methods for bioinformatics and sequence alignments and quasi alignments. First, it is the splitting of the sequences, as they are read, into, let’s say, ‘a’ De Bruijn graph. This graph consists of the k-mers, their neighborhoods, and of course the walks or paths through the graph that constitute optimal criteria and local maxima of course for traversal and contig/walk/path maximization. Typically, a search through the De Bruijn structure may be Breadth-First to find optimal depths for traversal of the path through the De Bruijn structure, optimizing for creating some sequence. This leads to read collapse along the sequence unidirectionally (bidirectionally in a unidimensional space) along the sequence space.

Prose

bioinformatics

python

Basic Python 2

16 minute read

Published:

Skip the description, let’s get to the code!